Integration of Non-Coding RNA and mRNA Profiles Reveals the Mechanisms of Rumen Development Induced by Different Types of Diet in Calves

Abstract

Selecting suitable feed types and understanding the gastrointestinal digestive mechanism are helpful for the growth and health of calves in intensive dairy farming. However, the effects on rumen development of changing the molecular genetic basis and the regulatory mechanism by using different feed types are still unclear. Nine 7-day-old Holstein bull calves were randomly divided into GF (concentrate), GFF (alfalfa: oat grass = 3:2) and TMR (concentrate: alfalfa grass: oat grass: water = 0.30:0.12:0.08:0.50) diet experiment groups. Rumen tissue and serum samples were collected for physiological and transcriptomic analysis after 80 days. The results showed that serum α-amylase content and ceruloplasmin activity were significantly higher in the TMR group, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis ncRNAs and mRNAs were significantly enriched in the pathways of rumen epithelial development and stimulated rumen cell growth, including the Hippo signaling pathway, Wnt signaling pathway, thyroid hormone signaling pathway, ECM–receptor interaction and the absorption of protein and fat. The circRNAs/lncRNA-miRNAs-mRNA networks constructed, including novel_circ_0002471, novel_circ_0012104, TCONS_00946152, TCONS_00960915, bta-miR-11975, bta-miR-2890, PADI3 and CLEC6A, participated in metabolic pathways of lipid, immune system, oxidative stress and muscle development. In conclusion, the TMR diet could improve rumen digestive enzyme activities, stimulate rumen nutrient absorption and stimulate the DEGs related to energy homeostasis and microenvironment balance, and is thus better than the GF and GFF diets for promoting rumen growth and development.

A Preliminary Study of the Potential Molecular Mechanisms of Individual Growth and Rumen Development in Calves with Different Feeding Patterns

“…The study further demonstrated that feeding only concentrated feed to calves could cause a series of inflammatory reactions, lead to immune system disorders, and affect the normal growth and development of the rumen, but there were certain differences from previous research results at the genetic level [93]. Although the study found reliable results in rumen microorganisms body metabolism, due to the small number of test samples and the lack of relevant data on rumen microbial metabolism, further research will be needed in the individual growth, rumen development and disease of calves.…”

Microbial Metagenomes and Host Transcriptomes Reveal the Dynamic Changes of Rumen Gene Expression, Microbial Colonization and Co-Regulation of Mineral Element Metabolism in Yaks from Birth to Adulthood

“…RNA-seq-based host transcriptome analysis has been extensively studied in ruminants to understand changes in rumen tissue with age, types of diet, weaning, and metabolic disorders at the molecular level [19,[85][86][87]. The rumen separates the individual ruminant from the microbiome, but also interacts with the microbiome, thereby affecting the immune status and physiology of the host.…”

Postnatal Growth and Development of the Rumen: Integrating Physiological and Molecular Insights

“…Transcriptomic analyses suggested that transforming growth factor-β might be another hormone mediating the growth of rumen epithelium from pre-weaned to post-weaned calves [131]. Similarly, integrated analysis of differentially expressed long non-coding RNAs and mRNAs revealed thyroid hormone as another candidate hormone that mediates rumen development in postnatal animals [132,133].…”